I am not sure I truly understand the situation -- so let me re-iterate what I see from you post.-->
(a) you receive a stipend as a Grad TA -- this amount shows up on your W-2---yes?
(b) to record the tuition waiver, you received a 1098-T with Box -1 showing the portion of Tuition that you (?) paid - why is there an amount that you paid since tuition was waived?
(c) Box 5 of 1098-T shows the total tuition waiver amount as scholarship.
Therefore the question is whom pays the taxes (if any ) for the difference amount between Box-1 and Box-5 ?
Cannot really answer till I hear from you on my questions.
Generally I would have assumed that Box 1 would show the total amount of Tuition Paid ( irrespective of source). And Box 5 would show the total amount of scholarship. This would show that all of the scholarship was used for qualified educational purposes and therefore not taxable ( to the extent used for qualified educational expenses ).
